[2023-06-13 09:31:41,866] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:31:41,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:31:41,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference
[2023-06-13 09:31:43,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:31:43,408] [INFO] Task started: Prodigal
[2023-06-13 09:31:43,408] [INFO] Running command: gunzip -c /var/lib/cwl/stgd773f21a-ddab-4a68-be84-90cd3628bcce/GCA_022755855.1_ASM2275585v1_genomic.fna.gz | prodigal -d GCA_022755855.1_ASM2275585v1_genomic.fna/cds.fna -a GCA_022755855.1_ASM2275585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:31:44,576] [INFO] Task succeeded: Prodigal
[2023-06-13 09:31:44,576] [INFO] Task started: HMMsearch
[2023-06-13 09:31:44,576] [INFO] Running command: hmmsearch --tblout GCA_022755855.1_ASM2275585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/reference_markers.hmm GCA_022755855.1_ASM2275585v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:31:44,810] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:31:44,811] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd773f21a-ddab-4a68-be84-90cd3628bcce/GCA_022755855.1_ASM2275585v1_genomic.fna.gz]
[2023-06-13 09:31:44,825] [INFO] Query marker FASTA was written to GCA_022755855.1_ASM2275585v1_genomic.fna/markers.fasta
[2023-06-13 09:31:44,825] [INFO] Task started: Blastn
[2023-06-13 09:31:44,826] [INFO] Running command: blastn -query GCA_022755855.1_ASM2275585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/reference_markers.fasta -out GCA_022755855.1_ASM2275585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:31:45,319] [INFO] Task succeeded: Blastn
[2023-06-13 09:31:45,324] [INFO] Selected 14 target genomes.
[2023-06-13 09:31:45,324] [INFO] Target genome list was writen to GCA_022755855.1_ASM2275585v1_genomic.fna/target_genomes.txt
[2023-06-13 09:31:45,326] [INFO] Task started: fastANI
[2023-06-13 09:31:45,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgd773f21a-ddab-4a68-be84-90cd3628bcce/GCA_022755855.1_ASM2275585v1_genomic.fna.gz --refList GCA_022755855.1_ASM2275585v1_genomic.fna/target_genomes.txt --output GCA_022755855.1_ASM2275585v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:31:49,080] [INFO] Task succeeded: fastANI
[2023-06-13 09:31:49,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:31:49,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:31:49,086] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 09:31:49,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 09:31:49,086] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.6715	129	140	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.6542	129	140	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 09:31:49,088] [INFO] DFAST Taxonomy check result was written to GCA_022755855.1_ASM2275585v1_genomic.fna/tc_result.tsv
[2023-06-13 09:31:49,089] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:31:49,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:31:49,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/checkm_data
[2023-06-13 09:31:49,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:31:49,103] [INFO] Task started: CheckM
[2023-06-13 09:31:49,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022755855.1_ASM2275585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022755855.1_ASM2275585v1_genomic.fna/checkm_input GCA_022755855.1_ASM2275585v1_genomic.fna/checkm_result
[2023-06-13 09:32:01,834] [INFO] Task succeeded: CheckM
[2023-06-13 09:32:01,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:32:01,860] [INFO] ===== Completeness check finished =====
[2023-06-13 09:32:01,860] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:32:01,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022755855.1_ASM2275585v1_genomic.fna/markers.fasta)
[2023-06-13 09:32:01,861] [INFO] Task started: Blastn
[2023-06-13 09:32:01,861] [INFO] Running command: blastn -query GCA_022755855.1_ASM2275585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0326e6e1-70e9-43b9-a8fd-d88b36864036/dqc_reference/reference_markers_gtdb.fasta -out GCA_022755855.1_ASM2275585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:32:02,458] [INFO] Task succeeded: Blastn
[2023-06-13 09:32:02,463] [INFO] Selected 16 target genomes.
[2023-06-13 09:32:02,464] [INFO] Target genome list was writen to GCA_022755855.1_ASM2275585v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:32:02,465] [INFO] Task started: fastANI
[2023-06-13 09:32:02,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgd773f21a-ddab-4a68-be84-90cd3628bcce/GCA_022755855.1_ASM2275585v1_genomic.fna.gz --refList GCA_022755855.1_ASM2275585v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022755855.1_ASM2275585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:32:07,008] [INFO] Task succeeded: fastANI
[2023-06-13 09:32:07,011] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:32:07,011] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000160875.1	s__Lactobacillus iners	98.6542	129	140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
--------------------------------------------------------------------------------
[2023-06-13 09:32:07,013] [INFO] GTDB search result was written to GCA_022755855.1_ASM2275585v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:32:07,014] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:32:07,017] [INFO] DFAST_QC result json was written to GCA_022755855.1_ASM2275585v1_genomic.fna/dqc_result.json
[2023-06-13 09:32:07,017] [INFO] DFAST_QC completed!
[2023-06-13 09:32:07,018] [INFO] Total running time: 0h0m25s